Crystal structure of a hexameric LonA protease bound to three ADPs

Experimental Data Snapshot

  • Resolution: 3.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.4 of the entry. See complete history


Structural Insights into the Allosteric Operation of the Lon AAA+ Protease

Lin, C.-C.Su, S.-C.Su, M.-Y.Liang, P.-H.Feng, C.-C.Wu, S.-H.Chang, C.-I.

(2016) Structure 24: 667-675

  • DOI: https://doi.org/10.1016/j.str.2016.03.001
  • Primary Citation of Related Structures:  
    4YPL, 4YPN

  • PubMed Abstract: 

    The Lon AAA+ protease (LonA) is an evolutionarily conserved protease that couples the ATPase cycle into motion to drive substrate translocation and degradation. A hallmark feature shared by AAA+ proteases is the stimulation of ATPase activity by substrates. Here we report the structure of LonA bound to three ADPs, revealing the first AAA+ protease assembly where the six protomers are arranged alternately in nucleotide-free and bound states. Nucleotide binding induces large coordinated movements of conserved pore loops from two pairs of three non-adjacent protomers and shuttling of the proteolytic groove between the ATPase site and a previously unknown Arg paddle. Structural and biochemical evidence supports the roles of the substrate-bound proteolytic groove in allosteric stimulation of ATPase activity and the conserved Arg paddle in driving substrate degradation. Altogether, this work provides a molecular framework for understanding how ATP-dependent chemomechanical movements drive allosteric processes for substrate degradation in a major protein-destruction machine.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease555Meiothermus taiwanensisMutation(s): 1 
Gene Names: lonA1lon
Find proteins for A0A059VAZ3 (Meiothermus taiwanensis)
Explore A0A059VAZ3 
Go to UniProtKB:  A0A059VAZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059VAZ3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
H [auth B],
K [auth F],
M [auth D]
C10 H15 N5 O10 P2
Query on 4KZ

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
J [auth C]
L [auth F]
N [auth D]
G [auth A],
I [auth B],
J [auth C],
L [auth F],
N [auth D],
O [auth E]
C22 H23 B N4 O4
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.044α = 90
b = 169.128β = 90
c = 135.361γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description